Finding the right rabbit to pull out of the hat: data management in CSIRO

CSIRO is one of the world’s largest and most diverse research agencies with staff located literally from one end of Australia to the other as well as internationally. As both a creator and a consumer of research data, CSIRO faces considerable data management challenges. To this end, the development of the CSIRO Data Management Service (DMS) Repository is a pivotal step in the right direction for managing CSIRO-generated data, third-party data and establishing vital links with research community portals such as Research Data Australia and the Atlas of Living Australia. From metadata mapping to collector and conversion tools, this presentation will discuss the experiences of the CSIRO Information Management & Technology (IM&T) team in applying new services and technologies to address the challenges of discovering, exchanging and re-using research data

Community-owned resource persons for malaria vector control: enabling factors and challenges in an operational programme in Dar es Salaam, United Republic of Tanzania.

BACKGROUND: Community participation in vector control and health services in general is of great interest to public health practitioners in developing countries, but remains complex and poorly understood. The Urban Malaria Control Program (UMCP) in Dar es Salaam, United Republic of Tanzania, implements larval control of malaria vector mosquitoes. The UMCP delegates responsibility for routine mosquito control and surveillance to community-owned resource persons (CORPs), recruited from within local communities via the elected local government. METHODS: A mixed method, cross-sectional survey assessed the ability of CORPs to detect mosquito breeding sites and larvae, and investigated demographic characteristics of the CORPs, their reasons for participating in the UMCP, and their work performance. Detection coverage was estimated as the proportion of wet habitats found by the investigator which had been reported by CORP. Detection sensitivity was estimated as the proportion of wet habitats found by the CORPS which the investigator found to contain Anopheles larvae that were also reported to be occupied by the CORP. RESULTS: The CORPs themselves perceived their role as professional rather than voluntary, with participation being a de facto form of employment. Habitat detection coverage was lower among CORPs that were recruited through the program administrative staff, compared to CORPs recruited by local government officials or health committees (Odds Ratio = 0.660, 95% confidence interval = [0.438, 0.995], P = 0.047). Staff living within their areas of responsibility had > 70% higher detection sensitivity for both Anopheline (P = 0.016) and Culicine (P = 0.012): positive habitats compared to those living outside those same areas. DISCUSSION AND CONCLUSIONS: Improved employment conditions as well as involving the local health committees in recruiting individual program staff, communication and community engagement skills are required to optimize achieving effective community participation, particularly to improve access to fenced compounds. A simpler, more direct, less extensive community-based surveillance system in the hands of a few, less burdened, better paid and maintained program personnel may improve performance and data quality

Right Here Right Now (RHRN) pilot study: testing a method of near-real-time data collection on the social determinants of health

Background: Informing policy and practice with up-to-date evidence on the social determinants of health is an ongoing challenge. One limitation of traditional approaches is the time-lag between identification of a policy or practice need and availability of results. The Right Here Right Now (RHRN) study piloted a near-real-time data-collection process to investigate whether this gap could be bridged. Methods: A website was developed to facilitate the issue of questions, data capture and presentation of findings. Respondents were recruited using two distinct methods – a clustered random probability sample, and a quota sample from street stalls. Weekly four-part questions were issued by email, Short Messaging Service (SMS or text) or post. Quantitative data were descriptively summarised, qualitative data thematically analysed, and a summary report circulated two weeks after each question was issued. The pilot spanned 26 weeks. Results: It proved possible to recruit and retain a panel of respondents providing quantitative and qualitative data on a range of issues. The samples were subject to similar recruitment and response biases as more traditional data-collection approaches. Participants valued the potential to influence change, and stakeholders were enthusiastic about the findings generated, despite reservations about the lack of sample representativeness. Stakeholders acknowledged that decision-making processes are not flexible enough to respond to weekly evidence. Conclusion: RHRN produced a process for collecting near-real-time data for policy-relevant topics, although obtaining and maintaining representative samples was problematic. Adaptations were identified to inform a more sustainable model of near-real-time data collection and dissemination in the future

Role of intraganglionic transmission in the trigeminovascular pathway

Migraine is triggered by poor air quality and odors through unknown mechanisms. Activation of the trigeminovascular pathway by environmental irritants may occur via activation of transient receptor potential ankyrin 1 (TRPA1) receptors on nasal trigeminal neurons, but how that results in peripheral and central sensitization is unclear. The anatomy of the trigeminal ganglion suggests that noxious nasal stimuli are not being transduced to the meninges by axon reflex but likely through intraganglionic transmission. Consistent with this concept, we injected calcitonin gene-related peptide, adenosine triphosphate, or glutamate receptor antagonists or a gap junction channel blocker directly and exclusively into the trigeminal ganglion and blocked meningeal blood flow changes in response to acute nasal TRP agonists. Previously, we observed chronic sensitization of the trigeminovascular pathway after acrolein exposure, a known TRPA1 receptor agonist. To explore the mechanism of this sensitization, we utilized laser dissection microscopy to separately harvest nasal and meningeal trigeminal neuron populations in the absence or presence of acrolein exposure. mRNA levels of neurotransmitters important in migraine were then determined by reverse transcription polymerase chain reaction. TRPA1 message levels were significantly increased in meningeal cell populations following acrolein exposure compared to room air exposure. This was specific to TRPA1 message in meningeal cell populations as changes were not observed in either nasal trigeminal cell populations or dorsal root ganglion populations. Taken together, these data suggest an important role for intraganglionic transmission in acute activation of the trigeminovascular pathway. It also supports a role for upregulation of TRPA1 receptors in peripheral sensitization and a possible mechanism for chronification of migraine after environmental irritant exposure

Measuring Potential Dermal Transfer of a Pesticide to Children in a Child Care Center

Currently, the major determinants of children’s exposure to pesticides are not fully understood, and approaches for measuring and assessing dermal exposure in a residential setting have not been sufficiently evaluated. In one approach, dermal exposure is estimated using empirically derived transfer coefficients. To assess the feasibility of using this approach for assessing children’s exposure to pesticides, we conducted a study was conducted in a child care center that had a preexisting contract with a pest control service for regular monthly pesticide applications. Children in the selected child care center were monitored using full-body cotton garments to measure dermal loading. Pesticide residues on classroom surfaces were measured in the areas where the children spent time. Measured surface-wipe loadings ranged from 0.47 to 120 ng/cm(2), and total garment loadings ranged from 0.5 to 660 pg/cm(2). The garment and surface loading measurements were used to calculate dermal-transfer coefficients for use in assessing children’s residential exposure to pesticides. Dermal-transfer coefficients calculated using these data range from approximately 10 to 6,000 cm(2)/hr. The wide range in these values demonstrates the importance of developing standard surface-measurement protocols if this approach is to be used to assess dermal exposure in a residential environment. The upper-range values resulting from this study were found to be similar to the default value used by the U.S. Environmental Protection Agency to assess children’s dermal exposures resulting from contact with indoor surfaces

Couple-based psychosexual support following prostate cancer surgery: results of a feasibility pilot randomized control trial

Surgery for prostate cancer can result in distressing side effects such as sexual difficulties, which are associated with lower levels of dyadic functioning. The study developed and tested an intervention to address sexual, relational, and emotional aspects of the relationship after prostate cancer by incorporating elements of family systems theory and sex therapy

Interleukin 12 (IL-12) is increased in tumour bearing human liver and expands CD8C and CD56C T cells in vitro but not in vivo

Human liver is enriched with CD8CT- and CD3CCD56C natural T (NT)-lymphocytes, important anti-tumour effectors, similar to murine NKTs. IL-12 promotes anti-tumour functions of NKTs. We quantified IL-12 and CD56C/CD8CT lymphocytes in normal and tumour bearing liver. We also examined the effect of IL-12 on the expansion/activation of peripheral blood cells in vitro. IL-12 was detected in normal (n ¼ 13, median 2032 pg/100 mg protein) and increased in tumour bearing liver (n ¼ 9, 3678 pg, p!0:01). Infiltrating monocytes appear to be the principal producers. Culture with IL-12 selectively expanded CD8CT and CD3CCD56CNT cells and polarised their cytokine responses to Th1-type. However, there was no in vivo expansion of these cells in tumour bearing liver. Changes observed in culture required addition of IL-2. We therefore quantified IL-2 in hepatic tissue. IL-2 was detected in normal liver (median 4700 pg/100 mg protein). Surprisingly, there was no increase in tumour-infiltrated liver (4910 pg). The presence of IL-12 may create an environment in healthy liver that promotes the accumulation of CD8CT and CD56CNT cells. Therefore, the development of metastases in the presence of high levels of IL-12 may be due to an insufficient IL-12 response. Alternatively, lack of IL-2 rather than a defect in IL-12, may be responsible for insufficient expansion/activation of tumour specific cytotoxic T lymphocytes

Interleukin 12 (IL-12) is increased in tumour bearing human liver and expands CD8C and CD56C T cells in vitro but not in vivo

Human liver is enriched with CD8CT- and CD3CCD56C natural T (NT)-lymphocytes, important anti-tumour effectors, similar to murine NKTs. IL-12 promotes anti-tumour functions of NKTs. We quantified IL-12 and CD56C/CD8CT lymphocytes in normal and tumour bearing liver. We also examined the effect of IL-12 on the expansion/activation of peripheral blood cells in vitro. IL-12 was detected in normal (n ¼ 13, median 2032 pg/100 mg protein) and increased in tumour bearing liver (n ¼ 9, 3678 pg, p!0:01). Infiltrating monocytes appear to be the principal producers. Culture with IL-12 selectively expanded CD8CT and CD3CCD56CNT cells and polarised their cytokine responses to Th1-type. However, there was no in vivo expansion of these cells in tumour bearing liver. Changes observed in culture required addition of IL-2. We therefore quantified IL-2 in hepatic tissue. IL-2 was detected in normal liver (median 4700 pg/100 mg protein). Surprisingly, there was no increase in tumour-infiltrated liver (4910 pg). The presence of IL-12 may create an environment in healthy liver that promotes the accumulation of CD8CT and CD56CNT cells. Therefore, the development of metastases in the presence of high levels of IL-12 may be due to an insufficient IL-12 response. Alternatively, lack of IL-2 rather than a defect in IL-12, may be responsible for insufficient expansion/activation of tumour specific cytotoxic T lymphocytes

MyI-Net: Fully Automatic Detection and Quantification of Myocardial Infarction from Cardiovascular MRI Images

A "heart attack" or myocardial infarction (MI), occurs when an artery supplying blood to the heart is abruptly occluded. The "gold standard" method for imaging MI is Cardiovascular Magnetic Resonance Imaging (MRI), with intravenously administered gadolinium-based contrast (late gadolinium enhancement). However, no "gold standard" fully automated method for the quantification of MI exists. In this work, we propose an end-to-end fully automatic system (MyI-Net) for the detection and quantification of MI in MRI images. This has the potential to reduce the uncertainty due to the technical variability across labs and inherent problems of the data and labels. Our system consists of four processing stages designed to maintain the flow of information across scales. First, features from raw MRI images are generated using feature extractors built on ResNet and MoblieNet architectures. This is followed by the Atrous Spatial Pyramid Pooling (ASPP) to produce spatial information at different scales to preserve more image context. High-level features from ASPP and initial low-level features are concatenated at the third stage and then passed to the fourth stage where spatial information is recovered via up-sampling to produce final image segmentation output into: i) background, ii) heart muscle, iii) blood and iv) scar areas. New models were compared with state-of-art models and manual quantification. Our models showed favorable performance in global segmentation and scar tissue detection relative to state-of-the-art work, including a four-fold better performance in matching scar pixels to contours produced by clinicians